Published in Syst Biol on March 16, 2013
Unlocking the vault: next-generation museum population genomics. Mol Ecol (2013) 1.77
Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One (2014) 1.45
Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One (2015) 1.42
Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol (2014) 1.03
The use of museum specimens with high-throughput DNA sequencers. J Hum Evol (2014) 0.99
Genomic repeat abundances contain phylogenetic signal. Syst Biol (2014) 0.88
Character displacement of Cercopithecini primate visual signals. Nat Commun (2014) 0.84
Mitogenomics of the Old World monkey tribe Papionini. BMC Evol Biol (2014) 0.83
Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Mol Biol Evol (2015) 0.81
Discovery and full genome characterization of a new SIV lineage infecting red-tailed guenons (Cercopithecus ascanius schmidti) in Kibale National Park, Uganda. Retrovirology (2014) 0.81
Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis). BMC Genomics (2015) 0.80
The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res (2015) 0.78
Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens. PLoS One (2016) 0.75
No need to replace an "anomalous" primate (Primates) with an "anomalous" bear (Carnivora, Ursidae). Zookeys (2015) 0.75
Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus. BMC Genomics (2016) 0.75
Localized population divergence of vervet monkeys (Chlorocebus spp.) in South Africa: Evidence from mtDNA. Am J Phys Anthropol (2015) 0.75
Mitochondrial metagenomics: letting the genes out of the bottle. Gigascience (2016) 0.75
Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecol Evol (2017) 0.75
Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections. PLoS One (2017) 0.75
Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) (2017) 0.75
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol (2008) 38.22
Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform (2008) 22.07
A draft sequence of the Neandertal genome. Science (2010) 19.55
Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol (2002) 15.22
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol (2012) 11.97
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol (2009) 7.59
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc (2010) 6.39
Field guide to next-generation DNA sequencers. Mol Ecol Resour (2011) 5.93
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst Biol (2008) 5.89
Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79
Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol (2009) 5.64
A molecular phylogeny of living primates. PLoS Genet (2011) 5.61
The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques (2000) 4.59
phangorn: phylogenetic analysis in R. Bioinformatics (2010) 4.57
A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution (2005) 3.45
Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One (2010) 3.35
The late Miocene radiation of modern Felidae: a genetic assessment. Science (2006) 3.35
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol (2008) 3.21
A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol (2009) 3.09
Likelihood methods for detecting temporal shifts in diversification rates. Evolution (2006) 2.95
Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst Biol (2011) 2.94
Back to the future: museum specimens in population genetics. Trends Ecol Evol (2007) 2.85
Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet (2010) 2.70
Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol (1988) 2.59
The Neandertal genome and ancient DNA authenticity. EMBO J (2009) 2.46
Organization and dynamics of human mitochondrial DNA. J Cell Sci (2004) 2.45
Detecting the Geographical Pattern of Speciation from Species-Level Phylogenies. Am Nat (2000) 2.31
North Pacific seasonality and the glaciation of North America 2.7 million years ago. Nature (2005) 2.20
Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol (2004) 2.18
Palaeobotanical studies from tropical Africa: relevance to the evolution of forest, woodland and savannah biomes. Philos Trans R Soc Lond B Biol Sci (2004) 2.17
Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J Hum Evol (2005) 2.05
Natural hybridization in primates: one evolutionary mechanism. Zoology (Jena) (2006) 1.88
A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour (2009) 1.75
Analysis of high-throughput ancient DNA sequencing data. Methods Mol Biol (2012) 1.67
Explosive Pleistocene diversification and hemispheric expansion of a "great speciator". Proc Natl Acad Sci U S A (2009) 1.65
Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution (2005) 1.65
Mitochondrial phylogeography of baboons (Papio spp.): indication for introgressive hybridization? BMC Evol Biol (2009) 1.65
High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res (2010) 1.56
Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol Biol (2009) 1.52
Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst Biol (2011) 1.37
Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol (2009) 1.35
A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes. PLoS Pathog (2007) 1.25
A comparison of anubis baboons, hamadryas baboons and their hybrids at a species border in Ethiopia. Folia Primatol (Basel) (1973) 1.24
Natural hybridization generates mammalian lineage with species characteristics. Proc Natl Acad Sci U S A (2010) 1.21
Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol (2011) 1.21
Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Res (2011) 1.18
A mobile element-based evolutionary history of guenons (tribe Cercopithecini). BMC Biol (2007) 1.18
X-chromosomal window into the evolutionary history of the guenons (Primates: Cercopithecini). Mol Phylogenet Evol (2005) 1.15
Introgressive hybridization in southern African baboons shapes patterns of mtDNA variation. Am J Phys Anthropol (2010) 1.08
Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons. PLoS One (2010) 1.07
Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini). J Hum Evol (2004) 1.05
Behavioral variation and reproductive success of male baboons (Papio anubis x Papio hamadryas) in a hybrid social group. Am J Primatol (2008) 0.95
Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. Mol Biol Evol (2009) 0.93
Phylogenomics of African guenons. Chromosome Res (2008) 0.91
Miocene cercopithecoidea from the Tugen Hills, Kenya. J Hum Evol (2010) 0.90
Terrestrial adaptations in the postcranial skeletons of guenons. Am J Phys Anthropol (1994) 0.89
Comparing chromosomal and mitochondrial phylogenies of the Indriidae (Primates, Lemuriformes). Chromosome Res (2011) 0.80
Comparison of responses to alarm calls by patas (Erythrocebus patas) and vervet (Cercopithecus aethiops) monkeys in relation to habitat structure. Am J Phys Anthropol (2002) 0.79
A fertile hybrid between two Cercopithecus spp. in the Budongo forest, Uganda. Folia Primatol (Basel) (1968) 0.76
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Analysis of one million base pairs of Neanderthal DNA. Nature (2006) 6.17
Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A (2007) 6.12
Genetic analyses from ancient DNA. Annu Rev Genet (2004) 6.09
Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79
Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc Natl Acad Sci U S A (2004) 5.41
DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A (2008) 4.97
Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci (2005) 4.58
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res (2011) 4.33
From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res (2007) 4.26
Preserving the evolutionary potential of floras in biodiversity hotspots. Nature (2007) 3.93
Angiosperm phylogeny based on matK sequence information. Am J Bot (2003) 3.80
Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci (2004) 3.53
Genomic sequencing of Pleistocene cave bears. Science (2005) 3.40
A draft genome of Yersinia pestis from victims of the Black Death. Nature (2011) 3.18
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res (2009) 3.09
Complete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches. Syst Biol (2009) 2.92
Oligocene CO2 decline promoted C4 photosynthesis in grasses. Curr Biol (2007) 2.88
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One (2012) 2.60
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
The Neandertal genome and ancient DNA authenticity. EMBO J (2009) 2.46
Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot (2002) 2.35
C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr Biol (2007) 2.21
An extreme case of plant-insect codiversification: figs and fig-pollinating wasps. Syst Biol (2012) 2.20
Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc Natl Acad Sci U S A (2011) 2.15
Cross-cultural comparison of three medicinal floras and implications for bioprospecting strategies. J Ethnopharmacol (2011) 2.06
60 million years of co-divergence in the fig-wasp symbiosis. Proc Biol Sci (2005) 1.98
Building supertrees: an empirical assessment using the grass family (Poaceae). Syst Biol (2002) 1.95
Complex vocal imitation during ontogeny in a bat. Biol Lett (2009) 1.93
Environmental energy and evolutionary rates in flowering plants. Proc Biol Sci (2004) 1.84
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife (2013) 1.84
Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc Natl Acad Sci U S A (2002) 1.82
Genome-wide comparison of medieval and modern Mycobacterium leprae. Science (2013) 1.81
Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann Bot (2003) 1.79
Radiation in the Cape flora and the phylogeny of peacock irises Moraea (Iridaceae) based on four plastid DNA regions. Mol Phylogenet Evol (2002) 1.78
Learning about human population history from ancient and modern genomes. Nat Rev Genet (2011) 1.74
Speciation with gene flow on Lord Howe Island. Proc Natl Acad Sci U S A (2011) 1.70
Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European Neandertals. Curr Biol (2006) 1.69
Contrasted patterns of hyperdiversification in Mediterranean hotspots. Proc Natl Acad Sci U S A (2008) 1.58
High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res (2010) 1.56
Multiplex amplification of ancient DNA. Nat Protoc (2006) 1.49
Evidence of recent and continuous speciation in a biodiversity hotspot: a population genetic approach in southern African gladioli (Gladiolus; Iridaceae). Mol Ecol (2010) 1.49
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet (2013) 1.48
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci U S A (2014) 1.47
Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia). BMC Evol Biol (2010) 1.42
Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson. Ecol Lett (2015) 1.41
Phylogenies reveal predictive power of traditional medicine in bioprospecting. Proc Natl Acad Sci U S A (2012) 1.39
Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol (2008) 1.39
Testing Darwin's naturalization hypothesis in the Azores. Ecol Lett (2011) 1.36
A plea for DNA banking. Science (2004) 1.32
Causes of plant diversification in the Cape biodiversity hotspot of South Africa. Syst Biol (2011) 1.30
Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A (2014) 1.29
Environmental causes for plant biodiversity gradients. Philos Trans R Soc Lond B Biol Sci (2004) 1.26
Early axonopathy preceding neurofibrillary tangles in mutant tau transgenic mice. Am J Pathol (2007) 1.26
Unparalleled rates of species diversification in Europe. Proc Biol Sci (2010) 1.25
FReD: the floral reflectance database--a web portal for analyses of flower colour. PLoS One (2010) 1.25
Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biol (2011) 1.24
Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC Plant Biol (2011) 1.22
Diversification of land plants: insights from a family-level phylogenetic analysis. BMC Evol Biol (2011) 1.21
Virus progeny of murine cytomegalovirus bacterial artificial chromosome pSM3fr show reduced growth in salivary Glands due to a fixed mutation of MCK-2. J Virol (2011) 1.20
Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol (2014) 1.20
The effects of above- and belowground mutualisms on orchid speciation and coexistence. Am Nat (2011) 1.18
Origin and diversification of the Greater Cape flora: ancient species repository, hot-bed of recent radiation, or both? Mol Phylogenet Evol (2008) 1.16
Genetic characterization of the ABO blood group in Neandertals. BMC Evol Biol (2008) 1.15
Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources. J Vis Exp (2009) 1.14
First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One (2012) 1.11
Environment, area, and diversification in the species-rich flowering plant family Iridaceae. Am Nat (2005) 1.10
Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae). Ann Bot (2011) 1.10
Assessing internal support with large phylogenetic DNA matrices. Mol Phylogenet Evol (2003) 1.10
Phylogeny and evolution of basils and allies (Ocimeae, Labiatae) based on three plastid DNA regions. Mol Phylogenet Evol (2004) 1.09
Genomic insights into the origin of farming in the ancient Near East. Nature (2016) 1.07
A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America. Mol Phylogenet Evol (2007) 1.07
Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One (2012) 1.06
The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae). PLoS One (2011) 1.04
Systematics and evolution of tribe Sinningieae (Gesneriaceae): evidence from phylogenetic analyses of six plastid DNA regions and nuclear ncpGS. Am J Bot (2003) 1.02
Dissecting the plant-insect diversity relationship in the Cape. Mol Phylogenet Evol (2008) 1.02
Yersinia pestis: new evidence for an old infection. PLoS One (2012) 1.02
Female-biased dispersal and patrilocal kin groups in a mammal with resource-defence polygyny. Proc Biol Sci (2007) 1.00
The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study. Evolution (2007) 0.99
Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata). PLoS One (2013) 0.98
How sympatric is speciation in the Howea palms of Lord Howe Island? Mol Ecol (2009) 0.96
Biogeographical and phylogenetic origins of African fig species (Ficus section Galoglychia). Mol Phylogenet Evol (2006) 0.95
The mahogany family "out-of-Africa": divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Mol Phylogenet Evol (2006) 0.95
Genetic and morphological divergences in the cosmopolitan deep-sea amphipod Eurythenes gryllus reveal a diverse abyss and a bipolar species. PLoS One (2013) 0.95
Technical aspects of the WaveLight FS200 femtosecond laser. J Refract Surg (2010) 0.94
In contrast to many other mammals, cetaceans have relatively small hippocampi that appear to lack adult neurogenesis. Brain Struct Funct (2013) 0.94
Identification of forensically important Sarcophaga species (Diptera: Sarcophagidae) using the mitochondrial COI gene. Int J Legal Med (2012) 0.93
Development of a complex floral trait: The pollinator-attracting petal spots of the beetle daisy, Gorteria diffusa (Asteraceae). Am J Bot (2009) 0.93
Convergent evolution of floral signals underlies the success of Neotropical orchids. Proc Biol Sci (2013) 0.92
Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol (2009) 0.91
Behavioral sterility of hybrid males in acoustically communicating grasshoppers (Acrididae, Gomphocerinae). J Comp Physiol A Neuroethol Sens Neural Behav Physiol (2007) 0.91
Apomixis and reticulate evolution in the Asplenium monanthes fern complex. Ann Bot (2012) 0.90
Diversification rates and chromosome evolution in the most diverse angiosperm genus of the temperate zone (Carex, Cyperaceae). Mol Phylogenet Evol (2012) 0.90
Functional analysis of human and chimpanzee promoters. Genome Biol (2005) 0.89
Shared pattern of endocranial shape asymmetries among great apes, anatomically modern humans, and fossil hominins. PLoS One (2012) 0.87